```edpiecepoint(1)             General Commands Manual            edpiecepoint(1)

NAME
edpiecepoint - edit a list of piece coordinates

SYNOPSIS
edpiecepoint  [options] [input_file] output_file

DESCRIPTION
This program allows one to "edit" a list of piece coordinates, or a
list of integer point coordinates, in three ways: 1) The set of Z val-
ues may be mapped, one-to-one, to any arbitrary new set of Z values;
and 2) The X, Y or Z coordinates of all pieces or points may be shifted
by a constant.  3) The overlap between pieces can be changed.  In addi-
tion, one can create a new piece list for single frame images or mon-
taged images.  The pieces can be ordered in rows, in columns, or even
progressing in Z first for each montage position.

The remapping of Z values is specified by a list of values (comma-sepa-
rated ranges, e.g. 0-3,5-7).  This list must have the same number of Z
values as in the input list of Z values.  The Z values in the input
list will be mapped one-to-one onto the new list.  Enter "/" to take
the input list without modification Enter numbers between -999 and -990
to delete points with a particular Z value; e.g. if the input list has
Z values from 0 to 9, entering 0-4,-999,5-8 will delete all points with
Z between 4.5 and 5.5, and shift the Z of points with Z greater then
5.5 down by 1.  If the input list has Z from 0-19, entering
0-9,-999--990 will remove all points with Z from 10 to 19.  Enter -1 to
replace each Z value with its negative.

When you create a new piece list, you control the overlap between
pieces by entering a spacing instead.  This spacing is the frame size
minus the overlap; e.g., for a size of 2048 and an overlap of 10%, one
would enter 2048 - 204 = 1844.  Spacing can be measured by taking the
difference between the coordinates of corresponding points in adjacent
pieces.  For example, if a feature is at an X coordinate of 1800 in one
piece and at 100 in the piece to the right, then the spacing in X is
1800 - 100 = 1700.  Enter a negative number for X spacing if pieces are
ordered from right to left, or a negative number for Y spacing if
pieces are ordered from top to bottom.  Enter / if you just have one
piece.

OPTIONS
Edpiecepoint uses the PIP package for input (see the manual page for
pip) and can still take sequential input interactively.  The follow-
ing options can be specified either as command line arguments (with the
-) or one per line in a command file or parameter file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.

-input (-i) OR -InputFile      File name
Input piece list or point file.  If this option is not entered
and -create is not entered, the first non-optional argument will
be used for an input file.

-output (-ou) OR -OutputFile   File name
Output piece list or point file.  If this option is not entered,
the second non-optional argument will be used if -create is not
entered; otherwise the first non-option argument will be used
for an output file.

-create (-cr) OR -CreateForSections      Integer
Number of sections to create a new piece list for

-pieces (-pi) OR -PiecesInXandY     Two integers
Number of pieces in X and Y in the newly created piece list

-spacing (-sp) OR -SpacingInXandY   Two integers
Spacing between the pieces in X and Y in the newly created piece
list.  Enter the negative of a spacing to have pieces coordi-
nates put out in inverse order, from high to low coordinates.
For how to determine the desired spacing, see above.

-columns (-co) OR -ColumnsOfPieces
Order pieces in a newly created piece list so that successive
pieces occur in columns (in Y) rather than in rows (in X).

-stacks (-st) OR -StacksOfPieces    Integer
Order pieces in a newly created piece list so that successive
pieces go through the entire set of Z values at each position in
X and Y.  Enter 1 to have pieces in order by Z, or -1 for pieces
in inverse order.  This option can be used together with the
-columns option.

-divide (-d) OR -DivideByBinning    Integer
This option can be used to make a new piece list that works with
binned images.  Rather than just dividing the existing coordi-
nates by the binning, the program determines a new overlap value
and makes sure that coordinates are regularly spaced apart.  To
do this, it needs the image sizes before and after binning,
entered with -size and -binned.

-overlap (-ov) OR -NewOverlapInXandY     Two integers
This option can be used to change the overlap between pieces in
a piece list.  Enter the new overlaps in X and Y, and enter the
size of the pieces with the -size option.

-size (-si) OR -SizeInXandY    Two integers
Size of pieces in X and Y.  This entry is required to adjust
overlap or to divide by binning; in the latter case enter the
full size of the unbinned images to which the input piece list
corresponds.

-binned (-b) OR -BinnedSizeInXandY       Two integers
New, binned size of pieces in X and Y (required to divide by
binning)

-new (-n) OR -NewZList    List of integer ranges
List of Z values to map old list to.  There must be as many val-
ues in this list as in the list of Z values to remap.  See notes
above on the contents of this list.

Amount to add to all coordinates in X, Y, and Z, after remapping

-param (-pa) OR -ParameterFile      Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.

-help (-h) OR -usage
Print help output

-StandardInput
Read parameter entries from standard input.

INTERACTIVE INPUT
If there are no command-line arguments, Edpiecepoint takes sequential
input the old way, with the following entries:

Name of input piece or point list file, or Return if none

IF you enter "Return", then the program will create a new piece
list.  Then make the following 4 entries:

Number of sections (N) for which to make piece coordinates.  The Z
coordinates will initially run from 0 to N-1, and the lower left X
and Y coordinates will be 0.

Number of pieces in X and in Y (enter / for 1,1)

Spacing between pieces in X and in Y.  See above.

0 if pieces progress along rows in the image file, or 1 if they
progress along columns.

Name of output piece or point list file

New list of Z values.  See above.

Amounts to add to all X, Y, and Z coordinates.  These values will be
added after the remapping of Z values, if any.

HISTORY
Written by David Mastronarde, 5/8/89

BUGS
Email bug reports to mast at colorado dot edu.

IMOD                                4.9.10                     edpiecepoint(1)
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